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package App::Sandy::Types; |
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# ABSTRACT: Moose type constraints for App::Sandy project |
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use Moose::Util::TypeConstraints; |
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our $VERSION = '0.22'; # VERSION |
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subtype 'My:IntGt0' |
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=> as 'Int' |
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=> where { $_ > 0 } |
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=> message { "Value must be an integer greater than zero, not '$_'" }; |
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subtype 'My:IntGe0' |
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=> as 'Int' |
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=> where { $_ >= 0 } |
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=> message { "Value must be an integer greater or equal to zero, not '$_'" }; |
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subtype 'My:NumGt0' |
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=> as 'Num' |
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=> where { $_ > 0 } |
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=> message { "Value must be a number greater than zero, not '$_'" }; |
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subtype 'My:NumGe0' |
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=> as 'Num' |
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=> where { $_ >= 0 } |
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=> message { "Value must be a number greater or equal to zero, not '$_'" }; |
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subtype 'My:NumHS' |
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=> as 'Num' |
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=> where { $_ >= 0 && $_ <= 1 } |
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=> message { "Value must be a number between zero and one, not '$_'" }; |
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subtype 'My:File' |
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=> as 'Str' |
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=> where { -f $_ } |
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=> message { "'$_' must be a file" }; |
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subtype 'My:Fasta' |
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=> as 'My:File' |
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=> where { $_ =~ /.+\.(fasta|fa|fna|ffn)(\.gz)*$/ } |
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=> message { "'$_' must be a fasta file: Check the extension (.fasta, .fa, .fna, .ffn - compressed, or not, by gzip, as in .fasta.gz etc)" }; |
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subtype 'My:Weight' |
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=> as 'HashRef' |
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=> where { exists $_->{down} && exists $_->{up} } |
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=> message { "'$_' is not a Weight object" }; |
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subtype 'My:Weights' |
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=> as 'ArrayRef[My:Weight]' |
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=> message { "'$_' is not a Weight object array" }; |
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subtype 'My:QualityP' |
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=> as 'Str'; |
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coerce 'My:QualityP' |
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=> from 'Str' |
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=> via { lc $_ }; |
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subtype 'My:QualityH' |
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=> as 'HashRef' |
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=> where { exists $_->{matrix} && exists $_->{deepth} && exists $_->{partil} } |
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=> message { "'$_' is not a valid quality hash" }; |
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subtype 'My:IdFa' |
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=> as 'HashRef' |
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=> where { exists $_->{seq} && exists $_->{size} } |
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=> message { "'$_' is not a valid fasta id" }; |
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subtype 'My:IdxFasta' |
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=> as 'HashRef[My:IdFa]' |
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=> message { "'$_' is not a valid indexed fasta" }; |
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subtype 'My:StrandBias' |
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=> as 'Str' |
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=> where { $_ eq 'plus' || $_ eq 'minus' || $_ eq 'random' } |
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=> message { "'$_' is not a valid strand-bias: 'plus', 'minus' or 'random'" }; |
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subtype 'My:SeqIdWeight' |
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=> as 'Str' |
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=> where { $_ eq 'length' || $_ eq 'same' || $_ eq 'count' } |
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=> message { "'$_' is not a valid seqid-weight: 'length', 'same' or 'count'" }; |
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subtype 'My:SeqType' |
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=> as 'Str' |
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=> where { $_ eq 'single-end' || $_ eq 'paired-end' } |
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=> message { "'$_' is not a valid sequencing-type: 'single-end' or 'paired-end'" }; |
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subtype 'My:CountLoopBy' |
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=> as 'Str' |
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=> where { $_ eq 'coverage' || $_ eq 'number-of-reads' } |
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=> message { "'$_' is not a valid count_loops_by: 'coverage' or 'number-of-reads'" }; |
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subtype 'My:Piece' |
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=> as 'HashRef' |
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=> where { exists $_->{ref} && exists $_->{start} && exists $_->{len} && exists $_->{pos} && exists $_->{offset} } |
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=> message { "Invalid piece inserted to piece_table" }; |
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subtype 'My:PieceTable' |
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=> as 'HashRef' |
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=> where { exists $_->{size} && exists $_->{table} && ref $_->{table} eq 'App::Sandy::PieceTable' } |
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=> message { "Invalid piece table entry" }; |
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subtype 'My:Format' |
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=> as 'Str' |
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=> where { $_ eq 'fastq' || $_ eq 'fastq.gz' || $_ eq 'bam' || $_ eq 'sam' } |
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=> message { "Invalid output format: '$_': 'fastq', 'fastq.gz', 'bam', 'sam'" }; |
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subtype 'My:Level' |
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=> as 'Int' |
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=> where { /^[1-9]$/ } |
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=> message { "Invalid compression level: '$_': 1-9"}; |
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1; ## --- end class App::Sandy::Types |
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__END__ |
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=pod |
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=encoding UTF-8 |
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=head1 NAME |
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App::Sandy::Types - Moose type constraints for App::Sandy project |
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=head1 VERSION |
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version 0.22 |
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=head1 AUTHORS |
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=over 4 |
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=item * |
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Thiago L. A. Miller <tmiller@mochsl.org.br> |
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=item * |
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J. Leonel Buzzo <lbuzzo@mochsl.org.br> |
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=item * |
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Felipe R. C. dos Santos <fsantos@mochsl.org.br> |
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=item * |
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Helena B. Conceição <hconceicao@mochsl.org.br> |
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=item * |
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Gabriela Guardia <gguardia@mochsl.org.br> |
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=item * |
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Fernanda Orpinelli <forpinelli@mochsl.org.br> |
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=item * |
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Pedro A. F. Galante <pgalante@mochsl.org.br> |
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=back |
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=head1 COPYRIGHT AND LICENSE |
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This software is Copyright (c) 2018 by Teaching and Research Institute from SÃrio-Libanês Hospital. |
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This is free software, licensed under: |
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The GNU General Public License, Version 3, June 2007 |
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=cut |